Wellington District Health Board says "exceptionally high demand" for Covid-19 vaccinations and boosters has seen some sites run short of doses.
More than 41,000 booster doses were administered yesterday, as the gap between second and third doses of the vaccine was shortened to four months.
RNZ has spoken to people who have been been unable to get a walk-in booster in Wellington as some pharmacies run dry - with one woman turned away from three vaccination sites.
Jenny said she and at least 60 people waiting in line were turned away by pharmacies, who said they only had enough supply to vaccinate people with bookings.
She said she was concerned that it had been so hard to get a booster.
"I just wonder how many [more] days before I will get it. I'm most concerned, I'm actively seeking it out, the expectations were raised that they were available for walk-ups but they haven't delivered for me. It is frustrating."
Capital and Coast DHB Covid-19 response general manager Chris Mitchell told RNZ the soaring demand had contributed to temporary supply issues at some vaccination sites.
He said vaccine doses were being redistributing between sites to plug the gaps where possible.
"There will be plenty of doses available and no one will miss out, but we recognise that people may need to arrange an alternative time if they can't get their booster at the time and place they prefer," he said in a statement.
"We ask everyone to be patient and kind to staff at vaccination clinics. We expect to be back to business as usual within the next 48 hours."
Mitchell said it was encouraging to see so much enthusiasm in the region for booster doses.
Royal College of General Practitioners medical director Bryan Betty said the rollout was off to a roaring start.
"It's probably more than I expected to be honest, I mean for the holiday season when a lot of people are still away, I think that's an incredibly good result.
"It's very, very important that people get the booster vaccine once they reach the four month mark, and that's what's really important, it needs to be four months since their second dose of the vaccine."
Online bookings for booster doses open on 17 January.
Almost a million people became eligible for booster doses yesterday.